Error when trying to read in phosphorylated threonine

[hannahbaumann]

The CDK2 protein (from the PLB) has a phosphorylated threonine and when I try and read it in I'm getting this error:

protein = openfe.ProteinComponent.from_pdb_file("../01_protein/crd/protein.pdb")

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[4], line 1
----> 1 protein = openfe.ProteinComponent.from_pdb_file("../01_protein/crd/protein.pdb")

File ~/gufe/gufe/components/proteincomponent.py:106, in ProteinComponent.from_pdb_file(cls, pdb_file, name)
     90 """
     91 Create ``ProteinComponent`` from PDB-formatted file.
     92 
   (...)
    103     the deserialized molecule
    104 """
    105 openmm_PDBFile = PDBFile(pdb_file)
--> 106 return cls._from_openmmPDBFile(
    107     openmm_PDBFile=openmm_PDBFile, name=name
    108 )

File ~/gufe/gufe/components/proteincomponent.py:219, in ProteinComponent._from_openmmPDBFile(cls, openmm_PDBFile, name)
    217         resn = a.GetMonomerInfo().GetResidueName()
    218         resind = int(a.GetMonomerInfo().GetResidueNumber())
--> 219         raise ValueError(
    220             "I don't know this Ion or something really went "
    221             f"wrong! \t{atom_name}\t{resn}\t-{resind}\t"
    222             f"connectivity{connectivity}"
    223         )
    224 elif default_valence > connectivity:
    225     fc = - (default_valence - connectivity)  # negative charge

ValueError: I don't know this Ion or something really went wrong! 	N	TPO	-160	connectivity0

Is there a way to fix this?

Here is the input
https://github.com/openforcefield/protein-ligand-benchmark/blob/main/data/cdk2/01_protein/crd/protein.pdb

[richardjgowers]

@hannahbaumann https://github.com/OpenFreeEnergy/pdbinf/blob/main/notebooks/tpo_load.ipynb

[richardjgowers]

So pdbinf will give you a rdkit.Mol then you'll make the gufe.ProteinComponent from that. Isn't an option from the cli yet, it would need #135

[hannahbaumann]

Awesome, yes that worked!